Mercurial > repos > miller-lab > genome_diversity
annotate rank_pathways.xml @ 10:9b92372de9f6
rename snp to gsSnp, sap to gdSap
| author | Richard Burhans <burhans@bx.psu.edu> |
|---|---|
| date | Tue, 04 Sep 2012 12:49:53 -0400 |
| parents | e29f4d801bb0 |
| children |
| rev | line source |
|---|---|
| 0 | 1 <tool id="gd_calc_freq" name="Rank" version="1.0.0"> |
| 2 <description>affected KEGG pathways</description> | |
| 3 | |
| 4 <command interpreter="python"> | |
| 5 #if str($output_format) == 'a' | |
| 6 calctfreq.py | |
| 7 #else if str($output_format) == 'b' | |
| 8 calclenchange.py | |
| 9 #end if | |
| 10 "--loc_file=${GALAXY_DATA_INDEX_DIR}/gd.rank.loc" | |
| 11 "--species=${input.metadata.dbkey}" | |
| 12 "--input=${input}" | |
| 13 "--output=${output}" | |
| 14 "--posKEGGclmn=${input.metadata.kegg_path}" | |
| 15 "--KEGGgeneposcolmn=${input.metadata.kegg_gene}" | |
| 16 </command> | |
| 17 | |
| 18 <inputs> | |
|
10
9b92372de9f6
rename snp to gsSnp, sap to gdSap
Richard Burhans <burhans@bx.psu.edu>
parents:
7
diff
changeset
|
19 <param name="input" type="data" format="gdSap" label="Table"> |
| 0 | 20 <validator type="metadata" check="kegg_gene,kegg_path" message="Missing KEGG gene code column and/or KEGG pathway code/name column metadata. Click the pencil icon in the history item to edit/save the metadata attributes" /> |
| 21 </param> | |
| 22 <param name="output_format" type="select" label="Output format"> | |
| 23 <option value="a" selected="true">ranked by percentage of genes affected</option> | |
| 24 <option value="b">ranked by change in length and number of paths</option> | |
| 25 </param> | |
| 26 </inputs> | |
| 27 | |
| 28 <outputs> | |
| 29 <data name="output" format="tabular" /> | |
| 30 </outputs> | |
| 31 | |
| 32 <tests> | |
| 33 <test> | |
|
10
9b92372de9f6
rename snp to gsSnp, sap to gdSap
Richard Burhans <burhans@bx.psu.edu>
parents:
7
diff
changeset
|
34 <param name="input" value="test_in/sample.gdSap" ftype="gdSap" /> |
| 0 | 35 <param name="output_format" value="a" /> |
| 36 <output name="output" file="test_out/rank_pathways/rank_pathways.tabular" /> | |
| 37 </test> | |
| 38 </tests> | |
| 39 | |
| 40 <help> | |
| 41 **What it does** | |
| 42 | |
| 43 This tool produces a table ranking the pathways based on the percentage | |
| 44 of genes in an input dataset, out of the total in each pathway. | |
| 45 Alternatively, the tool ranks the pathways based on the change in | |
| 46 length and number of paths connecting sources and sinks. This change is | |
| 47 calculated between graphs representing pathways with and without excluding | |
| 48 the nodes that represent the genes in an input list. Sources are all | |
| 49 the nodes representing the initial reactants/products in the pathway. | |
| 50 Sinks are all the nodes representing the final reactants/products in | |
| 51 the pathway. | |
| 52 | |
| 53 If pathways are ranked by percentage of genes affected, the output is | |
| 54 a tabular dataset with the following columns: | |
| 55 | |
| 56 1. number of genes in the pathway present in the input dataset | |
| 57 2. percentage of the total genes in the pathway included in the input dataset | |
| 58 3. rank of the frequency (from high freq to low freq) | |
| 59 4. name of the pathway | |
| 60 | |
| 61 If pathways are ranked by change in length and number of paths, the | |
| 62 output is a tabular dataset with the following columns: | |
| 63 | |
| 64 1. change in the mean length of paths between sources and sinks | |
| 65 2. mean length of paths between sources and sinks in the pathway including the genes in the input dataset. If the pathway do not have sources/sinks, the length is assumed to be infinite (I) | |
| 66 3. mean length of paths between sources and sinks in the pathway excluding the genes in the input dataset. If the pathway do not have sources/sinks, the length is assumed to be infinite (I) | |
| 67 4. rank of the change in the mean length of paths between sources and sinks (from high change to low change) | |
| 68 5. change in the number of paths between sources and sinks | |
| 69 6. number of paths between sources and sinks in the pathway including the genes in the input dataset. If the pathway do not have sources/sinks, it is assumed to be a circuit (C) | |
| 70 7. number of paths between sources and sinks in the pathway excluding the genes in the input dataset. If the pathway do not have sources/sinks, it is assumed to be a circuit (C) | |
| 71 8. rank of the change in the number of paths between sources and sinks (from high change to low change) | |
| 72 9. name of the pathway | |
| 73 </help> | |
| 74 </tool> |